- ChimeraX-users - RBVI Mailing Lists

Can I change the curved cylinder into a straight one?
by 王超(Chao Wang) 28 Aug '22

28 Aug '22

Dear All,After displaying helix in cylinder mode, I found that it is curved by default. I would like to ask whether it can be changed to a straight shape with two ends as fulcrums or other straight way?Thanks,Chao.

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Questions on job status
by Will Grubbe 26 Aug '22

26 Aug '22

Hello, I've submitted a few jobs using ChimeraX and am wondering how to check the status of them. I just need to fill in a few residues in a protein complex with known sequence - where can I find the results when they are done? Thank you for your help, Will

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Imod map values
by HONG ZHAN 26 Aug '22

26 Aug '22

Dear all, It might be not a good question regarding chimeraX. I have a PEET generated averaged map and output of PEET is reversed vs. single particle maps. What is a good function to change the density of PEET output? I used newstack -multadd -1,0 function in imod, however it gave -137 level… Thanks! Hong

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3d-SNFG representation of glycans
by Varga Julia 26 Aug '22

26 Aug '22

Dear All, I am trying to visualize glycans in ChimeraX, however I cannot find the possibility to use either the 3D-SNFG, nor the filled planar representation. Am I overlooking something? Is there a possibility to do this? [image: image.png] Thank you very much! Best regards, Julia Varga

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Job or output file name when running Alphafold in ChimeraX?
by Rayees Mattoo 23 Aug '22

23 Aug '22

Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX? Best Rayees

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Segment Maps In ChimeraX
by Myers, Jonathan 22 Aug '22

22 Aug '22

Dear ChimeraX User Group, I'm trying to segment a map using an atomic model as a reference. To make my life easier for many of the operations I use in my work, I centered all of my structures to the origin of the session. However, when I want to segment out parts of my density, the original coordinates of the map are used for the various regions. I, therefore, can't use my centered structures as a reference as I had originally planned. I don't know if this is a bug or if this is intentionally programmed, but I am having a difficult time re-aligning the segmentation to my origin-based coordinate system. Is there a better way to do what I am trying to do or am I out of luck? Thank you. Shosholoza, Jonathan Myers

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request for true transparency support in .bild files
by Francois Berenger 22 Aug '22

22 Aug '22

Dear chimera hackers, In the old Chimera (not X), if I put two transparent spheres in a .bild file: one sphere can completely hide the other (e.g. a small one inside of a bigger one). While, if there was true transparency, no sphere should completely hide another. Is this better handled in ChimeraX? I _love_ .bild files, because it is so easy to generate them in order to annotate a 3D molecular system then view all of it (molecules + annotations) in Chimera. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Thanks a lot, F. PS: here is an example problematic .bild file for the old chimera --- .color green .transparency 0.750000 .sphere -0.542700 0.122500 -0.047867 1.500000 .sphere 1.060560 -1.270600 -0.236620 1.500000 .color orange .transparency 0.750000 .sphere 0.611100 -2.324200 -0.346200 1.250000 .sphere 1.108100 2.092000 0.140700 1.250000 .sphere -3.097400 0.651000 0.062700 1.250000 .color grey .transparency 0.750000 .sphere -0.542700 0.122500 -0.047867 1.500000 .sphere 1.060560 -1.270600 -0.236620 1.500000 .sphere -1.453700 2.784800 0.269900 1.500000 .sphere 3.272900 0.026100 -0.134900 1.500000 .sphere -2.354000 -1.959600 -0.245900 1.500000 ---

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Morph map parts transformation in a complex
by HONG ZHAN 22 Aug '22

22 Aug '22

Dear user group, I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same. Is there a way to do the map morph to transform different map parts in the complex? Many thanks! Hong

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Measure volume at multiple threshold levels not function
by Christian Tüting 22 Aug '22

22 Aug '22

Dear ChimeraX-Team, I have an issue with the volume measure tool. I would like to measure the volume at different thresholds. Using the gui mode, I can type the following: volume #1 level 1 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 volume #1 level 2 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 2.144e+06 So this is functional in principle. But I would like to run this in no gui mode, so the commands are ";" seperated. But, even in gui mode, I got the following: (threshold was set to 1 before executing) volume #1 level 1; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 volume #1 level 2; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 So the threshold level is not applied, prior to the measurement of the volume. And this is the same in the no-gui mode. I would like to check the volume at 5 different levels, but I got always the same value when executing: "/usr/libexec/UCSF-ChimeraX-daily/bin/ChimeraX --nogui --cmd 'open cryosparc_P42_J241_002_volume_map_sharp.mrc; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1' --exit" Is there any command, that the threshold level is somehow applied, and the measure volume is executed correctly? The problem is present in UCSF ChimeraX version: 1.4.dev202202240543 and UCSF ChimeraX version: 1.5.dev202207221833 Best Christian

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AlphaFold prediction of complex - results not downloaded
by Erik Werner 22 Aug '22

22 Aug '22

Ladies and Gentlemen, This weekend, I did an AlphaFold prediction run of the human Troponin complex (Troponin C, T and I, UniProt-Ids P63316, P45379, P19429, respectively) via a freshly installed ChimeraX (v 1.4)/Google Colab on macOS Catalina (10.15.7). It completed successfully after 8 hrs (see screenshot below) but I failed to locate the results. According to your tutorial (https://www.youtube.com/watch?v=6lXeCPuTePs and https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html) I was expecting the results in a Prediction#-folder within the Downloads folder, but ChimeraX had only saved the UniProt xml files there. Also, the notebook code indicated the download of a "results.zip" folder but that also cannot be found anywhere on the computer. What have I done wrong? Would I have to edit the notebook? Specify a folder, and where? And: can I still recover the results from Google Colab servers? I copied the notebook to my GoogleDrive but was unable to identify a run-id or anything specific to my run. I would really like to get this working as the prediction of complexes is such a fantastic resource! Many thanks for your help, Erik Werner, Berlin /--// //Dr. Erik Werner// //Paulstr. 36// //10557 Berlin// //Germany/

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Re: [chimerax-users] writing names of models as a text file
by Rangarajan, Amith 19 Aug '22

19 Aug '22

Dear Chimerax team, I want to access the names of the models in a individual chimerax session , i am not able to find a way to write them out as a txt file or to the log . please help me find a way to do this. thanks again for all your help, best amith

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Sym #1 command not executing
by John O'Brien 18 Aug '22

18 Aug '22

Hello, I am a new user to ChimeraX, and was doing the examples in the Quick Start Guide as practice. While following the Atomic Structure Commands, the "sym #1" command did not appear to produce the full table of symmetries, as described in the guide. Could you please help me with this? I have attached a screenshot of what I see to this email, hopefully that helps. Best, John O'Brien

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Re: [chimerax-users] Question about Coulombic scale bar in ChimeraX
by Elaine Meng 18 Aug '22

18 Aug '22

Hi Guipeun, This is the usual situation: The Color Key is not saying that -10 to +10 are the entire range in your structure, it is just showing how the color changes between -10 and +10. You would not change the values on the color key unless you also change the coloring. Any areas of the surface that have values beyond the range just get the same color as that end of the Color Key. I.e., all surface points with values below -10 (all the way down to the minimum for your surface -13.11) are the pure red shown at one end of the Color Key, and all surface points with values above 10 (up to the maximum for your surface +21) are the pure blue color shown at the other end. In between -10 and +10 the color gradually changes, and showing that change is the purpose of the Color Key. The tutorial uses "coulombic" with the default coloring, and the "key true" option in that command shows the values for that default coloring which are red for -10, white for 0, and blue for 10. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#k…> If you used different value/color settings in the command, then the key would appear with those different settings. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. it is recommended to send questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless you are including data that needs to remain private > On Aug 18, 2022, at 12:14 PM, Guipeun Kang <Guipeun.Kang(a)UTSouthwestern.edu> wrote: > > Dear Dr. Elaine Meng, > > My name is Guipeun Kang, a postdoctoral researcher in Dr. Ryan Hibbs at UT Southwestern medical center. > > I have a silly question about scale bar of Coulombic surface. > > I displayed Coulombic potential of 3eeb, which is an example on ChimeraX tutorial page. > https://www.rbvi.ucsf.edu/chimerax/features.html > > In the Log, Coulombic values are minimum -13.11 and maximum 20.86 for chain A, but the scale bar is ranged from -10 to 10 when I add color key as shown in the instructions. > https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#k… > > My question is: > When I type command "coulombic protein key true", the range of Coulombic surface of 3eeb is automatically reflected from -10 to 10? Or, should I manually change the scale bar range from -13 to 21 as shown in Log? > > I'm attaching a screenshot of ChimeraX Log and Color Key panel related to my question. > > I really appreciate your help, > Guipeun > > <image.png> > > UT Southwestern > Medical Center > The future of medicine, today.

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How to get back to original view after running resfit
by Rayees Mattoo 17 Aug '22

17 Aug '22

Hi, I am using resfit command. Is there a command or way to go back to the original view? Best, Rayees

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Rotate image on screen by 6 degrees?
by Robert Stroud 15 Aug '22

15 Aug '22

Is there a command that would rotate the image on screen (model and em map) by 6 degrees around the y axis? Im trying to make crossed eye stereo image for a paper, so I can then put the two images together in illustrator - as I see it Chimerax does not do crossed eye stereo, - and in stereo mode the center of rotation is not in the center of the image for me, so that the half images appear windowed differently on left and right? Thank you Robert Stroud stroud(a)msg.ucsf.edu <mailto:stroud@msg.ucsf.edu> 415 987 7535

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command question
by Kwangjun Lee 15 Aug '22

15 Aug '22

Hello, How can I adjust the position of the distance label? I figured out how to adjust the label for the residues. Thanks!

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Alternative locations
by Michael Bruist 15 Aug '22

15 Aug '22

In a demonstration page for students, I wish to show how the presence of the 2’OH on a ribonucleotide creates a clash at the active site of DNA polymerase. We are also trying to see if 2’OH’s create clashes within the primer. I have created a PDB file with deoxyribose as alternative location A and ribose as alternative location B. This works in original Chimera, but I am not getting it to work in ChimeraX. I am not able to specify the alternative atoms by their A and B designations. I do not see alternative locations in the hierarchy under target specification in the documentation. My PDB file is attached. Residues 106-113 have alternate locations included. The command “altlocs change A :113" does not seem to change anything, nor does changing the selection buttons in the Altexplorer. Mike Bruist mbruist(a)sju.edu

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docked UI
by Pranav Shah 13 Aug '22

13 Aug '22

Hi Team, Is there a way to make sure that some UI elements (eg. the chimerax python console) that I have enabled by calling from a custom startup script are pinned into the main window instead of appearing as floating windows? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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ISOLDE download
by Jason Mears 12 Aug '22

12 Aug '22

I am trying to download the ISOLDE bundle for my ChimeraX software. I have been unsuccessful thus far. The download starts, but it never completes the download. I have tried a number of times and logged in using my university credentials thinking that this might help. Nothing yet. I am running OS Monterrey (v 12.5). Any advice is appreciated. Thanks. - Jason Mears -- Associate Professor of Pharmacology Graduate Program Director, Pharmacology Center for Mitochondrial Diseases Case Western Reserve Univ SOM 216-368-3348 jason.mears(a)case.edu <mears.jason(a)case.edu>

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Drag select blanks view window
by Daniel Asarnow 09 Aug '22

09 Aug '22

In ChimeraX 1.3 and now 1.4 releases, I have an issue where control-click dragging to select causes the 3D viewer frame to black out. Everything else functions normally, including the select itself, although it is very difficult to use since the structure can't be seen. The select box *is* visible, but it's magenta instead of green. Afterwards things go back to normal if something was box selected, but if nothing was boxed then the 3D viewer remains blacked out until an interaction like moving the models/camera takes place. I'm on a 2021 M1 MacBook Pro with macOS 12.4. I was wondering if others have experienced this and if it's an M1 issue as this is the only machine I've seen exhibit the problem. Best, -da

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Distance between two residues
by Kwangjun Lee 07 Aug '22

07 Aug '22

Hello, Do you have a command that measures the distance between two residues? For example, I have a dimer model, and I want to measure the distance between /A:100 and /B:200 Thanks! Kwangjun Lee Ph.D. Candidate Department of Biomedical Sciences Florida State University College of Medicine 1115 W. Call Street Tallahassee, FL 32306 Tel: (850) 491-6985 Email: kwangjun.lee(a)med.fsu.edu<mailto:hyojeong.yong@med.fsu.edu>

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maps not on same grid in new ChimeraX?
by Moritz, Michelle 05 Aug '22

05 Aug '22

Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle

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Find Residues From Specified Residue Numbers Help
by Myers, Jonathan 05 Aug '22

05 Aug '22

Dear ChimeraX Users, I'm learning how to use the Python API and I found the set of ChimeraX recipes and am trying to use the code featured on the "Find Residues From Specified Residue Numbers" page. I've run into the following issue: NameError: name 'structure' is not defined. I'm not sure what I should be using as an input for the "structure.residues" argument so I have not changed that input. What "structure" should I be specifying? Any help would be greatly appreciated. Shosholoza, Jonathan Myers

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Color by Chemical Shift Perturbations
by Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare 05 Aug '22

05 Aug '22

Hi admin, I am trying to color the protein surface based on the chemical shift perturbations. As mentioned in the example published on March 15th, 2021, I was able to color the surface. However, I needed to add 6 levels, and I failed to do so. It was possible to define the levels and colors in chimera but I failed to do so in chimerax. Is there a way to solve this? Thank you Nadun Nadun Karunatilleke Ph.D. Candidate Dr. James Choy's Lab Department of Biochemistry Schulich School of Medicine & Dentistry Western University London, Ontario, Canada N6A 5C1

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Use different distances for several marker sets
by SHIQING LIAO 04 Aug '22

04 Aug '22

Dear community, I'm wondering if there is any way for me to color a volume density with different distances from several marker sets. Thank you for your help! Best, Shiqing

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Time-efficient python code for obtaining coordinates of atoms
by Shubham Devesh Ramgoolam 03 Aug '22

03 Aug '22

Hi all, I hope you are doing well. I am looking for a time-efficient way of obtaining the coordinates of specified residues. I cannot use the command getcrd as I need these coordinates in a python script for defining geometric objects (getcrd prints the output to the log). My attempt at this consisted of selecting all of the specified residues via run(session, ‘sel ...’), accessing that selection using selected_residues(session), and then, extracting the coordinates using .atoms.coords. The issue here is that run(session, ‘sel ...’) slows down if there are lots of specified residues. I tried bypassing the command ‘sel’ by first importing AtomSpecArg from chimerax.core.commands.atomspec and then using AtomSpecArg.parse('my residue_ID', session)[0].evaluate(session).atoms[0]. However, this is even slower. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Error message
by Kwangjun Lee 02 Aug '22

02 Aug '22

Hello, I was trying to find residues within the dimerization interface. I have watched the video https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s [https://i.ytimg.com/vi/TMcjEecFHaI/maxresdefault.jpg]<https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s> Evaluating AlphaFold protein-protein binding with ChimeraX<https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s> We show how to display AlphaFold predicted aligned error for residues at the binding interface between two proteins, encapsulin and ferritin, using ChimeraX.... www.youtube.com and follow the instructions but I got an error message and it seems others have the same issue with me. Is it a bug or did I do something wrong?? Thanks! Kwangjun Lee Ph.D. Candidate Department of Biomedical Sciences Florida State University College of Medicine 1115 W. Call Street Tallahassee, FL 32306 Tel: (850) 491-6985 Email: kwangjun.lee(a)med.fsu.edu<mailto:hyojeong.yong@med.fsu.edu>

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ChimeraX change chain IDs tool not available
by Rish, Anthony 02 Aug '22

02 Aug '22

Hello, I created a protein model with 9 separate chains and fit it to my experimental cryo-EM map. However, once I saved the new model, relative to the map, the chains were renamed to 1.1/A, 1.2/A… 1.9/A. This is no good since all chains now are labeled as A in the PDB file and programs like PyMol can’t tell the difference between the chains. I checked the ChimeraX user guide and there is supposed to be a tool for this exact problem called change chain IDs under the Tools->Structure Editing tabs, using the command changechains, but the tool is nowhere to be found. I’m running the current build of ChimeraX as of 8/2/22. How can I change the chain IDs of my model? Thanks, Anthony

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Sorting the required molecules in cvc file
by Dmitry Semchonok 02 Aug '22

02 Aug '22

Dear colleagues, I would like to find out about the possibilities. I have a model that contains apart from the other data, the pigment molecules – chlorophylls, carotenoids etc. Is there a way sort certain types of molecules in a *.cvc file by chimeraX so that the following information will be shown? Mol,Label,Element,X,Y,Z CHL,n 606,NC,267.342,151.989,253.363 CHL,n 606,MG,266.202,151.941,255.073 CHL,n 607,NB,275.512,153.952,252.428 CLA,n 610,MG,273.005,139.807,270.918 CLA,n 611,NB,288.916,127.885,266.725 Thank you! Kind regards, Dmitry

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Superposing protein structures
by Alicia Gardiol 01 Aug '22

01 Aug '22

We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer. - Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1) Thank you and best wishes. Alicia Gardiol, PhD

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Re: [chimerax-users] Model panel for multi-state objects of dimeric protein
by Elaine Meng 01 Aug '22

01 Aug '22

Hi Enrico, I haven't figured out why this doesn't work on your example (omitted since mailing to the list): close #1 & ~ #1.5 However, this works: delete #1 & ~ #1.5 Also if you didn't have other models (#2 etc.) that you were trying to keep you could just use delete ~#1.5 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2022, at 6:39 AM, Enrico Martinez <jmsstarlight(a)gmail.com> wrote: > > Hello Elaine, > I just faced the same problem that has been indicated in this topic > Thi time I am dealing with the monomeric multi-model complex obtained > from docking. > Here is the example of a pdb file consisted of 80+ docking poses. To > keep only the 1.5 sub-modeli've tried to use > close #1 & ~ #1.5 > but this produced nothing, while for other pdbs it works fine. Could > you tell me what's wrong with it? > Many thanks in advance > Cheers > Enrico

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Reduce figure size for export for publication
by Fossati, Andrea 01 Aug '22

01 Aug '22

Hi, How to best export figure at high-ish resolution to then add it to an already made illustrator panel? After some googling seems vector-based export is not possible so what is the recommended format and which resolution is best for 3x3 inch illustrator panel? At the moment I am exporting as TIFF with transparent background and size 5000 and supersampled 4 times to keep high res but the file has like 15Mb per structure which is not feasible/handy to modify. What is the suggested solution for paper figures? Best, Andrea Fossati, Ph.D Krogan Lab

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How to estimate 2dlabels fading?
by Edoardo D Imprima 01 Aug '22

01 Aug '22

Hi, Could you please explain more how the frames option works when changing 2dlabels? Let’s say I have 100 frames and I wish to have an arrow to appear at frame 10 for 5 frames? Many thanks in advance, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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Side view in command line
by HONG ZHAN 31 Jul '22

31 Jul '22

Hi all, I would like to setup a movie sequence using cxc file. It is very useful to setup in the UI window, however, any tricks could I use to set the clip plane in the command line to generate a view as in the attached picture? So that I can run my cxc file together with other actions? Many thanks! Hong [cid:12317B70-9FE5-4C25-933C-E56EF2888E9D]

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ChimeraX on Mac
by Lisa Käshammer 30 Jul '22

30 Jul '22

Dear developers, I have problems to get chimeraX to work on my computer. It had a previous version installed (1.1) which did not work anymore. So I removed that version and installed the newest version, however, it does not open. There is no error message so I am a bit lost at what I can do to resolve this issue. The macOS is 10.15.7. Thank you very much in advance. Best, Lisa

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command inquary
by Kwangjun Lee 29 Jul '22

29 Jul '22

Hello, Do you have any command that displays a selected region only? For example, I have a protein structure AA1 to AA300. I only want to display AA100 to AA200. Thanks!

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Re-scaling maps
by Nebojsa Bogdanovic 29 Jul '22

29 Jul '22

Hello, I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same. Is there any command in chimeraX or chimera to play with pix sizes to find the right one? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Application to enter the chimeraX user's group
by Xiaofeng CHU 28 Jul '22

28 Jul '22

Dear chimeraX team Sorry for the interruption. My name's Xiaofeng Chu, the phd candidate in Misha Kudryashev's group working on cryoET and structural biology. Could you please help me to enter the group of chimeraX users? So I can raise some questions about how to use it. Thank you very much in advance! And have a nice day. Best regards Xiaofeng -- Xiaofeng Chu (he/him) Ph.D. candidate in M. Kudryashev's research group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association 13125 Berlin, Germany

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Re: [chimerax-users] Assembling 2 proteins
by Elaine Meng 27 Jul '22

27 Jul '22

Hi Tata Santosh Rama Bhadra Rao, I already gave my suggestions in the previous message, so there is not really anything else I can do to teach you. Since you didn't give the details of all the steps that you tried and which step(s) gave results you didn't like, I can't tell you how to do it differently. My only idea is to go back to what I already suggested: you could use Matchmaker if you already had a pentamer, which you show in the bottom figures. So, following the instructions in my first reply, maybe you can take the chains shown in the top figures and match them onto the chains in the bottom figures to make the pentamer. However, that will only work if the proteins are very similar. If you did it already and it gave the bad result, maybe these proteins are not similar enough to use that approach. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 30, 2022, at 9:22 PM, SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> wrote: > > Hi Elaine, > > I tried doing and it came out like this. Final 2 figures are homomeric pentamers. First 2 are heteromers with 3A subunits (A, B, D chains) and 2D (C, E chains) subunits. Could you please help me or teach me assembling them properly. > > Thanking you, > > With best wishes, > Tata Santosh Rama Bhadra Rao, > PhD Scholar, > C/O Prof Helen Irving, > La Trobe university, > Bendigo, Vic-3550, > Australia. > Email: 19807877(a)students.latrobe.edu.au; > S.Tata(a)latrobe.edu.au > Phone: 0499263974 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wednesday, 25 May 2022 2:08 AM > To: SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Assembling 2 proteins > > Hello Tata Santosh Rama Bhadra Rao, > It all depends on what information you have already. If you don't know how the pentamer is supposed to look (how the proteins fit together), then there may not be enough information: ChimeraX is not going to predict the pentamer structure for you. > > You said "5 different proteins" which I interpret to mean they are not 5 copies of the same thing, that it is a heteropentamer and not a homopentamer. If they were 5 copies of the same thing (homopentamer), then you might be able to use the "sym" command to build it from one copy, if the input file contains symmetry matrices in the header, or you know the symmetry and can specify it separately: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> > > Otherwise: > You would only use Matchmaker if you also have an already-known structure of a similar pentamer. Then you would open the structure of that pentamer, open the structures of your five proteins (if the same one is multiple copies in the pentamer, you would open it multiple times), and then match each one of them to the similar subunit of the known pentamer. In other words, you would open 6 different PDB files and then use Matchmaker 5 times, once to match each of your proteins to the corresponding subunit of the pentamer. > > Just start Matchmaker (menu: Tools... Structure Comparison... Matchmaker) and in that dialog's Chain Pairing, choose "Specific chain(s) in reference structure with specific chain(s) in match structure". Choose one of your protein chains as the match structure and choose the corresponding chain in the known pentamer as the reference. Apply. Repeat with your second protein chain, etc. > > Here is the Matchmaker help with detailed explanations of all the options: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#top> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > On May 23, 2022, at 9:49 PM, SANTOSH RAMA BHADRA RAO TATA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi, > > > > I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it or if there is any other way to use the software and create pentamer please let me know. > > > > Thanking you, > > > > With best wishes, > > Tata Santosh Rama Bhadra Rao, > > PhD Scholar, > > C/O Prof Helen Irving, > > La Trobe university, > > Bendigo, Vic-3550, > > Australia. > > Email: 19807877(a)students.latrobe.edu.au; > > S.Tata(a)latrobe.edu.au > > Phone: 0499263974

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FitMap/FitList scripting
by Christian Tüting 27 Jul '22

27 Jul '22

Dear ChimeraX DevTeam, I am currently working on a project which requires fitting a single model multiple times in a map. This is easy doable with the global search parameter, and if n is big enough, all correct locations are found. My collegue Ioannis wrote you a couple of weeks ago to implement a copy function to the fitlist, but this includes only the statistics, but not the translation information of each model. This is only possible by clicking the button "Place Copy", which creates a copy of the model and applies the translation to this model. In the log, there is only the best model with the translation matrix, but if my map does have multiple correct locations, I'm missing this information. I extended the fitmap function in fitcmd.py, so it writes this to a file to the current location called fitmap.txt. This file contains all the statistics and the rotation/translation information. This might be handy for some users. Here is the code: f = open("fitmap.txt", "w") if len(flist) == 0: f.write("No fit found") else: for i, f0 in enumerate(flist): msg = f0.fit_message() f.write(f"Fit #{i+1}\n" + msg + "\n") f.close() Maybe you can include an option "to_text" (which is false by default), to actually add this functionality. Best Christian

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renumber command is unknown
by Kwangjun Lee 27 Jul '22

27 Jul '22

Hello, I am a new user of ChimeraX. I have tried to renumber AA but renumber is an unknown command. Is there any way that I renumber? For example, my current model starts C 1, I want to renumber it to C 20. Thanks for developing a great software.

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Fw: Cofactor Morph
by Colin Levy 27 Jul '22

27 Jul '22

Dr. Colin Levy c.levy(a)manchester.ac.uk Senior Technical Specialist (XRD) Manchester Institute of Biotechnology, Faculty of Science & Engineering Tel: +44 (0) 161 306 5168 The University of Manchester [cid:7fc572c6-1ad9-414b-9ab5-b520385d1c2d] ________________________________ From: Colin Levy Sent: 27 July 2022 12:58 To: chimerax-users(a)cgl.ucsf.edu Subject: Cofactor Morph Hello, I am new to Chimera X but looking to generate a morph between 4 states of my protein. The protein morph was very simple to achieve but I have been unable to figure out how to include the cofactor in my morph. The cofactor undergoes important rearrangements during the catalysis which I would like to capture in the movie. Thanks in advance, Colin Dr. Colin Levy c.levy(a)manchester.ac.uk Senior Technical Specialist (XRD) Manchester Institute of Biotechnology, Faculty of Science & Engineering Tel: +44 (0) 161 306 5168 The University of Manchester [cid:736ce72a-e048-40a9-88c8-978c7e7ced3b]

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movie recording while changing threshold level
by Elaine Meng 26 Jul '22

26 Jul '22

Hi Dmitry, You could do it using "perframe" with an embedded "volume level" command in your movie script. For example, the following gradually changes map #2 contour level from 2.5 to 0.5 over 50 image update frames: perframe "volume #2 level $1" range 2.5,0.5 frames 50 See the "perframe" help for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > > From: Dmitry Semchonok <semchonok(a)gmail.com> > Date: July 26, 2022 at 8:17:36 AM PDT > > Thank you very much for your tips. > Works as a charm. > How 1 more question if you please - > Is it possible to record a movie while your 3D map constantly changing its threshold volume level (from low to high - which is possible to set) ? > If yes, how? > Thank you in advance. > Sincerely, > Dmitry > >> >> Although it would still be nice to have a separate option, currently >> ndependent rotation can be scripted by using separate turn (or roll) >> commands as in this example from Tom Goddard: >> >> You can use the "model" and "center" options of the turn command to rotate >> each model about their own center. For example, rotating 2 models in 1 >> degree steps around the y axis for a total of 360 degrees >> >> movie record >> turn y 1 360 model #1 center #1 >> turn y 1 360 model #2 center #2 >> wait 360 >> movie encode side-by-side-spin.mp4 >> >> In this example the two models rotate at the same time. The turn command >> like other commands that create a motion returns immediately before any >> motion is done to allow you to start simultaneous motions. Then you use >> the "wait 360" command to wait until 360 frames have been rendered, then >> the .mp4 movie file is made. >>

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Adding H atoms
by Daniel VillanuevaAvalos 25 Jul '22

25 Jul '22

Hello, I am adding hydrogen atoms by entering addh#1 to the command line, and it works but when I export the pdb and import it into houdini, things are messed up. Sometimes it just doesn't show up and other times, just part of the structure shows up. Am I missing something? Thank you, Daniel.

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Re: [chimerax-users] Colab Modelled, but no PDB
by Tom Goddard 25 Jul '22

25 Jul '22

Hi Anthony, Predicting a dimer where the monomer is 1182 residues, so a total of 2364 residues is guaranteed to run out of memory on Colab or Colab Pro -- the GPUs they offer don't have enough memory (at most 16 GB). The web page on AlphaFold performance test cases shows that only an Nvidia A40 with 48 Gbytes of memory handles over 2100 residues. That web page gives results for running AlphaFold via ChimeraX on Colab, but also running AlphaFold installed on our machines at UCSF with either an A40 GPU or an RTX 3090 GPU (24 GB memory). The "no templates" means structure templates were not used when running on our UCSF machines. Tom > On Jul 24, 2022, at 1:35 AM, Anthony Morgan <anthony.morgan(a)pharm.ox.ac.uk> wrote: > > Dear Tom, > > Thanks so very much, this is low-hanging fruit for you, but invaluable for me as I am a newbie. Really appreciate it. The Test link is really illuminating too thank you. > > I had wanted to try a dimer of 1182 residues each, but I am doubting that this is going to work, even with the paid service. Agreed? > On the test page, one of the runs is annotated as “no templates”. I cannot see how you can add templates to the Alphafold panel. I only see Energy Minimization under Options. Am I missing something? > > I’ve now got the pdb of the one model, thank you. It’s obvious once it’s pointed out, but I couldn’t see the wood for the trees. > > Really appreciate your time. > > Kind regards, > > Anthony > > >> On 24 Jul 2022, at 00:37, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Anthony, >> >> AlphaFold predictions on Google Colab of 1200 amino acids often fail as you can see from test cases on this web page >> >> https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> >> >> With free Google Colab you often get a very old Nvidia K80 GPU with 12 Gbytes of memory. With Colab Pro ($10/month) I usually get an Nvidia P100 GPU with 16 Gbytes of memory which can handle slightly bigger proteins. You can check what GPU you got by pressing the "+ Code" button on the Google Colab window, then entering the command "!nvidia-smi" and pressing the play button, which gives output like this >> >> Sat Jul >> 23 23:28:55 2022 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 460.32.03 Driver Version: 460.32.03 CUDA Version: 11.2 | |-------------------------------+----------------------+----------------------+ | GPU Name >> Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 Tesla P100-PCIE... Off | 00000000:00:04.0 >> Off | 0 | | N/A 38C P0 34W / 250W | 16259MiB / 16280MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ >> >> >> To download a completed model after an AlphaFold error (typically out of memory), click on Files in the Google Colab window, then click on the predicted structure, "af1182_unrelaxed_model_1.pdb" in your image, and click the "..." to the right of the file and choose Download from the menu that appears. The file will then appear on your local computer in >> >> ~/Downloads/ChimeraX/AlphaFold/prediction_1 >> >> I'll see if I can add to the ChimeraX ColabFold output the GPU and also make it automatically download partial results in case an error occurs. >> >> Tom >> >> >>> On Jul 23, 2022, at 4:41 AM, Anthony Morgan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Dear All, >>> >>> I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. >>> >>> I’m running Chimera X 1.4 on a Macbook Air. >>> I want the predicted structure of a fairly large protein (1182 residues). >>> When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). >>> I re-ran the same sequence *without * Energy Minimization. >>> After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. >>> >>> Two questions: >>> >>> There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? >>> If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? >>> >>> Thanks for advice. >>> >>> Kind regards, >>> >>> Anthony >>> >>> <Screen Shot 2022-07-23 at 12.17.14.png> >>> >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> >

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Movie recording
by Dmitry Semchonok 25 Jul '22

25 Jul '22

Dear colleagues, I have several maps and models that I would like to spin around independently at once and record as a movie. How to do that? Thank you in advance. Kind regards, Dmitry

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Question about commands similar to openModel in Chimera
by Thu Nguyen 25 Jul '22

25 Jul '22

Good morning, I am editing a python script that previously used the command chimera.openModels.list(modelTypes=[chimera.Molecule])to return a list of open molecules. Do we have a similar command in ChimeraX or is there any other way to get a list of protein chains in ChimeraX? Thank you very much. Best regards, Thu

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Colab Modelled, but no PDB
by Anthony Morgan 23 Jul '22

23 Jul '22

Dear All, I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. * I’m running Chimera X 1.4 on a Macbook Air. * I want the predicted structure of a fairly large protein (1182 residues). * When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). * I re-ran the same sequence *without * Energy Minimization. * After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. Two questions: * There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? * If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? Thanks for advice. Kind regards, Anthony [cid:8B6C8DAE-A4C3-4F95-8B26-037B6B318679]

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Chimera X Runs But does Not Install
by Anthony Morgan 23 Jul '22

23 Jul '22

Dear All, I’m new to Chimera X, so I am probably doing something wrong. Hope you can help please. I have ‘installed' either v1.3 and, more recently, 1.4 on my Macbook Air (under OSX 10.15.5; 1.1GHz processor, Intel Iris Plus Graphics 1536 MB). * Whilst I can run Chimera X fine (the first time after ‘installing'), it doesn’t appear to be installed locally on my laptop (that I can find). * If I close the App and try and reopen in, it’s not local, and I have to run the Install .dmg every time I want to ‘run’ it, which takes an age. * Under Security > Privacy, Chimera has Full Disk Access. Is this normal behaviour? Thanks for any advice. Regards, Anthony

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Model panel for multi-state objects of dimeric protein
by Enrico Martinez 22 Jul '22

22 Jul '22

Dear ChimeraX users! I am working on the visualization of protein-ligand interactions obtained from docking. In the ChimeraX session I have a loaded session with 88 docking poses (consisting of each frame receptor and ligand) corresponded to the separate objects (1.1 .. to 1.88) >From this ensemble I need to keep only the X object from these multiple states. I have tried to use the following command: close #1 & ~ #1.x which works perfectly for the monomeric protein. But when I am dealing with the analysis of the dimer (with A and B chains) it does not work. Only close #1 still can be used to close ALL objects. Which command could be used to keep the selected state from the ensemble for both monomer and dimer in the same way? Many thanks in advance Cheers Enrico

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